AAV9-mediated functional screening for cardioprotective cytokines in Coxsackievirus-B3-induced myocarditis

Viral myocarditis (VM) is an important cause of heart failure (HF) in children and adults. However, the molecular determinants involved in cardiac inflammation and cardiomyocyte necrosis remain poorly characterized, and cardioprotective molecules are currently missing. Here, we applied an in vivo method based on the functional selection (FunSel) of cardioprotective factors using AAV vectors for the unbiased identification of novel immunomodulatory molecules in a Coxsackievirus B3 (CVB3)-induced myocarditis mouse model. Two consecutive rounds of in vivo FunSel using an expression library of 60 cytokines were sufficient to identify five cardioprotective factors (IL9, IL3, IL4, IL13, IL15). The screening also revealed three cytokines (IL18, IL17b, and CCL11) that were counter-selected and likely to exert a detrimental effect. The pooled overexpression of the five most enriched cytokines using AAV9 vectors decreased inflammation and reduced cardiac dilatation, persisting at 1 month after treatment. Individual overexpression of IL9, the top ranking in our functional selection, markedly reduced cardiac inflammation and injury, concomitant with an increase of anti-inflammatory Th2-cells and a reduction of pro-inflammatory Th17- and Th22-cells at 14 days post-infection. AAV9-mediated FunSel cardiac screening identified IL9 and other four cytokines (IL3, IL4, IL13, and IL15) as cardioprotective factors in CVB3-induced VM in mice.


Results
FunSel identifies IL9 as a potential cardioprotective agent in the sub-acute phase during VM. A schematic diagram of the FunSel technique for the in vivo selection of immunomodulating molecules in VM is shown in Fig. 1A. We generated a targeted AAV vector library using AAV9, which displays cardiotropic properties in mice 9 . The library contained an unbiased selection of interleukins (n = 30) and chemokines (n = 30), most of which are poorly investigated for their involvement in myocarditis. Each vector belonging to this collection included a unique DNA barcode allowing its unequivocal identification in the heart upon nextgeneration sequencing (NGS). FunSel consisted of a two-round screening process under the selective pressure of VM for 14 days. Vectors that overexpressed cardiomyocyte survival-promoting factors persisted longer in the infected myocardium than vectors expressing detrimental factors (or neutral factors) present in the same library. In FunSel, the selective pressure eventually induces the progressive enrichment of protective vectors, which is detected by analyzing the relative number of sequencing reads for each vector at the end of the process, compared to those in uninfected heart controls. The procedure eventually generates a comparative ranking list of the AAV9 library, based on the relative abundance of each vector in cardiac tissue after VM (3 pooled biological replicates/group, Supplementary Information 1, Table S1).
The ratio between relative AAV barcode frequency between transduced CVB3-infected and sham-control transduced hearts after the first round of in vivo selection with the AAV9 library (Pool 60) is shown in Fig. 1B.
By setting the barcode recovery ratio to the statistically expected value > 0.20, the NGS detected 46 cytokines. Sequencing reads for the remaining 14 cytokines were not deemed reliable, as they were not effectively packaged in Pool 60 ( Supplementary Information 2, Fig. S1A-C).
The six most enriched cytokines at the end of the first screening round were IL9, IL3, CCL26, IL15, IL4, IL13. We included these six cytokines in another AAV9 pool (Pool 15) for the second round of FunSel, together with other four cytokines that were also selected (CCL8, CCL7, CCL24, CCL25) and additional five depleted cytokines as controls (IL17b, CCL11, CXCL14, CCL20, 1L18; Table S1). We included depleted factors (and therefore potentially detrimental) in the pool to maintain a competitive selection among the factors in the pool (enriched vs. depleted) and to confirm their negative effect on cardiomyocyte survival upon CVB3-infection.
At the end of the second round of screening with Pool 15 (Fig. 1C), IL9, IL3, IL13, IL15, and IL4 were confirmed to be among the most abundantly recovered interleukins in CVB3-infected hearts (Table S1), with IL9 having the highest enrichment in both pools (1.95-and 36.70-fold change compared to sham controls, respectively; Fig. 1B,C). Factors depleted in the first round were confirmed as depleted in the second round. These included IL18, IL17b, and CCL11, with CCL11, also known as eotaxin 10 , reaching the lowest enrichment level in Pool 15 (0.30-fold change compared to sham controls, Fig. 1C).
Our investigations focused on IL9, IL3, IL13, IL15, and IL4. From the VM-enriched cytokines in Pool 15, we did not consider further CCL7, CCL24, and CCL26 as information of these chemokines is already available in acute myocarditis 11,12 . Synergic overexpression of IL9 plus IL3, IL4, IL13, and IL15 (Pool 5) is cardioprotective in the acute phase of VM. First, we investigated whether the synergic expression of the five enriched interleukins (IL-9, IL3, IL4, IL13, IL15; Pool 5) could be cardioprotective during the acute phase of VM and could also result later in beneficial effects against cardiac dysfunction.
Despite the beneficial effect on T lymphocyte recruitment and necrosis at 14 days, the individual overexpression of IL9 did not significantly change cardiac dimensions or systolic function at 35 days post-infection ( Fig. 8A,B, complete echocardiographic analysis in Supplementary Information 2, Table S3), although uninfected controls in both groups showed lower than expected ejection fractions, possibly due to anesthesia levels that also produced lower heart rates than in other experiments. Consistently, at 35 days post-infection, there was no significant difference in cardiac fibrosis (Fig. 8C,D).
Collectively, these findings indicate that IL9 overexpression increases the cardio-protective Th2 response in CVB3-myocarditis, decreasing at the same time the detrimental Th17 and Th22 populations at 14 days. However, IL9 alone is insufficient to determine long-term beneficial effects on cardiac function and prevent adverse cardiac remodeling.

Discussion
There is a definite need to develop novel therapies for viral myocarditis. Current treatments for this condition are only aimed to prevent or treat systolic dysfunction and arrhythmias and are essentially based on pathophysiological principles defined decades ago. Of note, none of the available drugs are specific for this condition, no biologic treatment is available (all the drugs are small molecules), and, most relevant, none of the therapies is aimed to target the pathological inflammatory response underlying myocarditis. In this study, we, therefore, wanted to  www.nature.com/scientificreports/ practice, co-infection of the same cell by more than one vector, and thus co-selection, can occur. However, these events do not prevent the identification of cardioprotective factors, but simply lowers the quantitative difference between selected and non-selected factors, without altering the ranking of the factors in the pool, as previously validated 8,15 . In this study viral infection and consequently cardiac inflammation act as a selective challenge, promoting an in vivo competitive process between putative beneficial and detrimental or non-effective genes within the same vector pool. Transduced cardiomyocytes dying as a consequence of viral infection or immunemediated cytotoxicity are rapidly removed from the myocardium, therefore, after 2 weeks of VM, DNA coding for neutral/detrimental factors are no longer detectable in the surviving cells. Barcodes from the surviving cardiomyocytes are recovered, and their relative abundance is revealed by a two-step PCR approach followed by next-generation sequencing, without introducing any bias, as previously validated 15 . Enriched vectors are expected to express protective proteins. FunSel is unique in permitting functional (as opposed to phenotypic) selection directly in vivo, is unbiased in terms of knowledge of the mechanism of action of the factors, and is competitive among the factors, eventually permitting their ranking for efficacy. In this study, the pooled AAV9-mediated overexpression of 60 cytokines in a human Coxsackievirus-B3-induced myocarditis mouse model allowed the identification of five cardioprotective interleukins (IL9, IL3, IL4, IL13, and IL15). The individual, AAV9-mediated overexpression of IL9, the most enriched cytokine in the screening, significantly decreased cardiac inflammation and necrosis 14 days after CVB3 infection. Along with decreased T lymphocyte recruitment, IL9 increased the number of cardiac anti-inflammatory Th2 lymphocytes while reducing detrimental Th17 and Th22 lymphocytes at 14 days.
IL9 is a pleiotropic cytokine and member of type II immune response, recently associated with the pathogenesis of inflammatory diseases and the preservation of immune tolerance 16,17 . The observed anti-inflammatory properties of IL9 overexpression are consistent with findings in IL9 knockout mice, in which its absence exacerbates cardiac inflammation and injury in VM 18 . We further explored T lymphocyte subpopulations upon IL9 overexpression. IL9 increased the number of cardiac Th2 lymphocytes, while it decreased Th17 and Th22 cells. Th2 lymphocytes may induce a humoral response towards viral infection that dampens adverse cardiac inflammation 19 , which occurs preferentially in female mice, resistant to VM 20 . Th2-secreted cytokines, such as IL4 and IL13 (both also enriched in our FunSel experiments), are crucial anti-inflammatory mediators by increasing A more persistent effect on cardiac fibrosis and systolic function at 35 days post-infection required the combined expression of IL9 with IL3, IL4, IL13, and IL15. IL9 is known to induce fibrosis in the chronic progression of several pathologies such as heart failure, and pulmonary and hepatic inflammatory diseases [23][24][25] , through the release of profibrotic tumor growth factor (TGF) 18,23,26 and connective tissue growth factor (CTGF) 27 . This may explain why prolonged IL9 overexpression, which is inevitable due to the persistence of AAV vectors, did not The selection of IL3, IL4, IL13, and IL15 by FunSel after VM selective pressure is in line with the established effects of these cytokines in other experimental settings. IL3 is protective against inflammatory arthritis 28 , while IL3 and IL4 synergistically reduce adverse inflammation by enhancing Th2 lymphocyte function 29 . Individually, IL4 is known to be cardioprotective in VM 30,31 , also enhancing natural killer (NK) anti-viral property 32 . IL13 attenuates cardiac damage, inducing anti-inflammatory (M2) macrophage differentiation and reducing fibrosis 33,34 . IL15 exert a direct anti-apoptotic function on cardiomyocytes 35 and cardioprotective activity in CVB3-induced myocarditis, reducing T lymphocyte and proinflammatory macrophage (M1) cardiac infiltration 36 . Thus, FunSel appears to have selected molecules endowed with therapeutic potential and have ranked them according to their individual potency.
The factors that were negatively selected in the screening also deserve attention. In the two screening experiments, IL17b, IL18, and CCL11 were consistently among the negatively enriched cytokines in the VM hearts, suggesting a possible detrimental role in cardiomyocyte survival during VM. IL17b is a homolog of IL17a, and both cytokines are signature factors of Th17 37 . IL17b stimulates the release of tumor necrosis factor (TNF) and IL1β and promotes heart failure in human myocarditis 13 . IL18 is a pro-inflammatory, IFNγ-inducing cytokine released by cardiomyocyte pyroptosis during cardiovascular diseases 38 and has been associated with cardiac inflammation during myocarditis induced by the encephalomyocarditis virus and by Trypanosoma infection 39,40 . Finally, CCL11, also known as eotaxin-1, is one of the main eosinophil and mast cell chemoattractants in cardiac fibrosis and mast cell activation in the host-to-graft response 10 . Thus, FunSel again appears to have appropriately selected against factors potentially exerting adverse effects also in VM.

Conclusions
Collectively, our data show that FunSel is an efficient method for the in vivo selection of immunomodulatory molecules that provide a survival advantage to myocardial tissue upon VM, specifically oriented to the acute phase of the disease when most of the T lymphocyte-related necrosis occurs. In terms of translation of these findings to therapy, it is worth noting that the few immunomodulating therapies that have reached clinical trials so far, including IL1β-blocking therapy 41 , or, more recently, IL1 receptor antagonist (IL1ra) administration 42 , are all based on the delivery of antagonists to potentially detrimental factors. Cytokines exerting a positive effect, such as IL9, can equally be considered for administration, either in the form of recombinant proteins or through the delivery of their mRNAs. This can be performed directly into the heart upon coronary catheterization or into the skeletal muscle for systemic protein production. The possibility of using the Stable Nucleic Acid

Sources.
All key resources and materials (including experimental animals, cell lines, antibodies and tools) are listed in Supplementary Information 3, Table S4, including manufacturer (when applicable), catalogue number, and Research Resource Identifiers (RRIDs) when applicable.
Generation of the AAV plasmid library. The plasmid library was generated as previously described 8,15 .
Briefly, all cDNAs were individually cloned into a modified pZac2.1 vector named pGi, under the control of the constitutive cytomegalovirus immediate-early (CMV-IE) promoter. At the 3'-end of each cDNA, a unique 10-bp sequence (barcode) was inserted, allowing detection upon barcode PCR amplification and sequencing. Barcodes differed for at least two base pairs to avoid errors during sequencing.

Production and purification of recombinant AAV (rAAV) vectors. The rAAV vectors used in this
study (http:// www. icgeb. org/ avu-core-facil ity) were produced as previously described 8,15 . Briefly, infectious AAV9 vector particles were generated in HEK293T cells, using a dual-plasmid co-transfection system for packaging. Viral stocks were obtained by CsCl (Sigma Aldrich, Belgium) gradient centrifugation, and rAAV titers were determined by measuring the copy number of viral genomes in pooled, dialyzed gradient fractions using Real-Time PCR. The vectors used in this study express the cloned cDNAs under the control of the constitutive cytomegalovirus immediate-early (CMV-IE) promoter, and all the viral stocks had titers between 10 12 and 10 13 viral genome (vg) per mL. All the animals were randomly allocated to the groups prior to unequivocal identification by P.C. No other confounding factors were taken into consideration. During animal allocation and experimental procedure no blinding procedure was implemented. During outcome assessment and data analysis a blinding procedure was performed, temporary erasing animal allocation within the experimental groups.
After 14 dpi, the animals were euthanized, and cardiac DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen, Belgium) from at least three animals per group and pooled in an equimolar amount. The DNA barcodes from the extracted DNA were amplified by two subsequent cycles of polymerase chain reaction (PCR) amplification, first with primers annealing to common regions on the plasmid vector (pGi Fw and pGi Rv, Supplementary Information 3, Table S4) and then with primers containing an Illumina index (Fw Illumina and True Seq adapter Index Rv, Supplementary Information 3, Table S4) required for sample multiplexing. Amplicons were purified from agarose gel and were sequenced on a HighSeq 2000 Illumina instrument. Next-generation sequencing (NGS) generated at least 1 million reads per sample, and samples with a number of reads < 5 were excluded from the analysis. An algorithm developed using the R software (version 4.0.4) allowed to assign the number of reads of each barcode to the correspondent gene name, considering an error of one bp to assign a correct barcode for unequivocal clone identification. For both Pool 60 and Pool 15, the barcode reading ratio in the original AAV pool lysate and the cardiac tissue was compared to the corresponding expected presence (1/60 and 1/15, respectively). Vectors with a barcode recovery ratio lower than 0.20 from any biological source were discarded from further analysis as not efficiently packaged (injected lysate) or not efficiently overexpressed vectors, respectively ( Supplementary Information 2, Fig. S1A-C). For all the other clones, an enrichment ratio between the CVB3-infected heart and not-infected cardiac tissue was determined. Factors with a ratio > 1.00 were considered positively enriched in CVB3-infected hearts. Those with a ratio < 1.00 were considered depleted in CVB3-infected hearts. The factors with a ratio equal to 1.00 were considered uninfluential. The screening cycle was repeated twice, first with Pool 60 and then with Pool 15.
Mice were euthanized by a ketamine/xylazine overdose, followed by thoracotomy and cardiac excision. All the hearts collected were washed and exposed to a 1 M KCl solution to induce a homogenous end of cardiac activity in diastole.
Histology and immunofluorescence. Cardiac tissue was fixed in a Tris-based buffer with zinc ions (BD, Belgium) for at least 48 h at room temperature and processed for further standard histological staining. Paraffinembedded cardiac sections (4-5 µm) were either stained with Harris-hematoxylin (VWR, Belgium) and Eosin (Sigma Aldrich, Belgium) to evaluate cardiac necrosis. Cardiac tissue was stained with a 0,1% Sirius Red (SR) F 3B (Sigma-Aldrich, Belgium) solution in 4% Picric Acid (Sigma-Aldrich, Belgium) to evaluate cardiac fibrosis.
All antibodies mentioned in this paragraph are listed in Supplementary Information 3, Table S4. Sections were immunolabeled with anti-mouse CD45 (1:100 dilution) for overall inflammation, CD68 (1:100 dilution) for macrophages and CD3 (1:50 dilution) for T lymphocyte recruitment. Tyramide signal amplification (Thermofisher Scientific, Belgium) was used for the CD45 and CD3 staining. In all fluorescent-based immuno-labeled sections, nuclei were counterstained with a 2.5 ng/mL DAPI solution (Sigma-Aldrich, Belgium).  47 . Myocardial necrosis was determined as a percentage of the sum of the necrotic areas per total cardiac area, with the aid of a 500,000 µm 2 /square grid centered on the image.
Immunostainings were quantified per myocardial cross-sectional area, as previously described 48 . Briefly, immune cell phenotyping was either determined as the number of CD45 (leukocytes), CD68 (monocytes), CD3 (T lymphocyte) positive cells per cardiac area, or as the percentage of positive-stained area per cardiac area when single-cell detection was not possible. Cardiac fibrosis was determined as the percentage of Sirius Red-stained collagen-positive area per cardiac area, with the aid of the color-threshold tool in ImageJ. A blinded observer (P.C.) performed both imaging and analysis.
Gene expression analysis. RNA was extracted from cardiac tissues and peritoneal exudates using the RNeasy Fibrous Tissue Mini Kit (Qiagen GmbH, Germany) following the manufacturer's instructions. For RT-PCR analysis, 1 µg of total RNA was reverse-transcribed into cDNA, using the Qiagen Quantitect ® Reverse transcription kit (Qiagen GmbH, Germany), following the manufacturer's instructions, and transcript levels were quantified using IQ SYBR-green supermix (Bio-Rad, UK) in a MyIQ iCycler (Bio-Rad, UK). Primers (Supplementary Information 3, Table S4) were designed to span exon-exon junctions of the genes of interest. In the case of non-detection datapoints of the corresponding animals were not plotted.
Transthoracic echocardiography and analysis. Cardiac function was assessed 35 days post-infection using an MS400 (18-38 MHz) transducer on a VEVO 2100 echocardiographer (Fujifilm VisualSonics, Netherlands), as previously described in other animal models 49 . Mice were anesthetized with 5% inhaled isoflurane (Cuphar, Oostkamp, Belgium) followed by 1.5% inhaled isoflurane to maintain them anesthetized. Animals were placed in a supine position on a heated pad to maintain the core body temperature between 37.5-37.7 °C, measured using a rectal probe. Throughout the procedure, both heart and respiratory rates were monitored continuously. Anterior (AW) and posterior wall (PW) thickness, and LV internal diameter (LVID) were assessed on a 2D M-Mode mid-ventricular short-axis (SAX) image. Cardiac output (CO), ejection fraction (EF), and endocardial volume were calculated automatically by the software. For all measurements, at least three stable cardiac cycles were analyzed and averaged. A blinded observer (P.C.) performed the analysis.
Cardiac immune population isolation. Mice were euthanized by ketamine/xylazine overdose, the chest cavity was exposed, and the right atrium was incised to allow blood outflow. The heart was immediately perfused with 5 mL ice-cold 0.05% EDTA in PBS into the left ventricle to wash away any residual blood from the cardiac vasculature and then excised. Both atria were removed, and the ventricles were placed in ice-cold PBS to isolate the immune cell cardiac population. The ventricles were minced into 1 mm 3 -size piece with a sterile surgical blade and placed in an enzymatic solution containing 2.5 mg/mL collagenase (Sigma-Aldrich, Belgium) for 40 min at 37 °C. After trituration, the single-cell suspension was layered on top of the Histopaque 1083 solution (Sigma-Aldrich, Belgium) to separate the immune from the non-immune fraction. The interphase, containing the immune fraction, was then rinsed with PBS. Blood samples underwent three cycles of erythrocyte lysis instead: specifically, blood was incubated 3' in ice with an Erylysis buffer (7.3 pH 0.15 M NH 4 Cl, 0.01 M NaHCO 3, and 0.1 mM EDTA in PBS) and washed with PBS afterward. Cells were centrifuged at 1600 RPM, and the supernatant was discarded for each lysis round. Finally, all the cell pellets were resuspended in 100 µL of flow cytometry buffer (0.1% BSA and 2 mM EDTA in PBS), and cells were counted. All the samples underwent further processing for flow cytometry analysis.
Flow cytometry analysis. The immune cell samples were transferred on a V-bottom 96-well plate and blocked with Fc block (anti-mouse CD16/CD32, 1:100 dilution, Thermofisher Scientific, Belgium) for 30 min on ice in the dark. Afterward, the samples were washed with flow cytometry buffer and centrifuged at 1600 RPM at 4 °C for 3 min. The pellets were then stained with the fluorochrome-conjugated antibodies for 30 min on ice in the dark. Afterward, the samples were washed with flow cytometry buffer and centrifuged at 1600 RPM at 4 °C for 3 min. Finally, all the samples were resuspended in 200 µL of flow cytometry buffer and analyzed on a CANTO II flow cytometer (Becton-Dickinson Benelux, Belgium). All antibodies used in this procedure were used at 1:100 dilution/10 6 cells stained and are listed in the Supplementary Information 3, Table S4.
Quantification and statistical analysis. All statistical analyses were performed using GraphPad Prism 9 (GraphPad Software, USA). Data are expressed as mean ± SEM. The normality of the distribution of all continuous variables was assessed using the Shapiro and Wilk test. When comparing only two groups, an unpaired Scientific Reports | (2022) 12:7304 | https://doi.org/10.1038/s41598-022-11131-w www.nature.com/scientificreports/ Student t test was used if groups passed the normality test, while a Mann-Whitney U test was used otherwise. When comparing two variables simultaneously (including treatment and pathology), a 2-way ANOVA with Tukey's correction was used if groups passed the normality test, while a Kruskal-Wallis test was used otherwise. Graphical data was shown as mean values with error bars indicating the SEM. Two-sided p-value p values of < 0.05 (*), < 0.01 (**) or < 0.001 (***); indicated significant differences between groups.
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